Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/v/vg/vg_1.30.0+ds-1+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/vg-1.30.0+ds-1+b164z05hpn/vg_1.30.0+ds-1+b1_amd64.buildinfo Get source package info: vg=1.30.0+ds-1 Source URL: http://snapshot.notset.fr/mr/package/vg/1.30.0+ds-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.49 bash=5.1-2+b1 bc=1.07.1-2+b2 binutils=2.35.2-2 binutils-common=2.35.2-2 binutils-x86-64-linux-gnu=2.35.2-2 bison=2:3.7.5+dfsg-1 bsdextrautils=2.36.1-7 bsdmainutils=12.1.7+nmu2 bsdutils=1:2.36.1-7 build-essential=12.9 bwa=0.7.17-6 bzip2=1.0.8-4 ca-certificates=20210119 cmake=3.18.4-2 cmake-data=3.18.4-2 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.75 debhelper=13.3.4 debianutils=4.11.2 dh-autoreconf=20 dh-strip-nondeterminism=1.11.0-1 diffutils=1:3.7-5 docbook=4.5-6 docbook-to-man=1:2.0.0-45 docbook-xml=4.5-9 docbook-xsl=1.79.2+dfsg-1 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.14-1 elfutils=0.183-3 fastahack=1.0.0+dfsg-7 file=1:5.39-3 findutils=4.8.0-1 flex=2.6.4-8 fontconfig=2.13.1-4.2 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:10.2.1-1 g++-10=10.2.1-6 gawk=1:5.1.0-1 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 grep=3.6-1 groff-base=1.22.4-6 gtk-doc-tools=1.33.2-1 gzip=1.10-4 help2man=1.48.2 hostname=3.23 icu-devtools=67.1-6 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 jq=1.6-2.1 libacl1=2.2.53-10 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2+b1 libasan6=10.2.1-6 libasm1=0.183-3 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbackward-cpp-dev=1.5-2 libbinutils=2.35.2-2 libblas3=3.9.0-3 libblkid-dev=2.36.1-7 libblkid1=2.36.1-7 libboost-program-options-dev=1.74.0.3 libboost-program-options1.74-dev=1.74.0-8 libboost-program-options1.74.0=1.74.0-8 libboost1.74-dev=1.74.0-8 libbrotli-dev=1.0.9-2+b2 libbrotli1=1.0.9-2+b2 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libbz2-dev=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcairo-gobject2=1.16.0-5 libcairo-script-interpreter2=1.16.0-5 libcairo2=1.16.0-5 libcairo2-dev=1.16.0-5 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcom-err2=1.46.2-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.2-2 libctf0=2.35.2-2 libcurl3-gnutls=7.74.0-1.1 libcurl4=7.74.0-1.1 libcurl4-gnutls-dev=7.74.0-1.1 libdatrie1=0.2.13-1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.256 libdebhelper-perl=13.3.4 libdeflate-dev=1.7-1 libdeflate0=1.7-1 libdisorder-dev=0.0.2+git20130809.8062ee1-2 libdisorder0=0.0.2+git20130809.8062ee1-2 libdivsufsort-dev=2.0.1-5 libdivsufsort3=2.0.1-5 libdpkg-perl=1.20.7.1 libdw-dev=0.183-3 libdw1=0.183-3 libelf-dev=0.183-3 libelf1=0.183-3 libexpat1=2.2.10-2 libexpat1-dev=2.2.10-2 libfastahack-dev=1.0.0+dfsg-7 libfastahack0=1.0.0+dfsg-7 libffi-dev=3.3-6 libffi7=3.3-6 libfile-stripnondeterminism-perl=1.11.0-1 libfml-dev=0.1+git20190320.b499514-1+b1 libfml0=0.1+git20190320.b499514-1+b1 libfontconfig-dev=2.13.1-4.2 libfontconfig1=2.13.1-4.2 libfontconfig1-dev=2.13.1-4.2 libfreetype-dev=2.10.4+dfsg-1 libfreetype6=2.10.4+dfsg-1 libfreetype6-dev=2.10.4+dfsg-1 libfribidi0=1.0.8-2 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-3 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgfortran5=10.2.1-6 libglib2.0-0=2.66.7-2 libglib2.0-bin=2.66.7-2 libglib2.0-data=2.66.7-2 libglib2.0-dev=2.66.7-2 libglib2.0-dev-bin=2.66.7-2 libgmp-dev=2:6.2.1+dfsg-1 libgmp10=2:6.2.1+dfsg-1 libgmpxx4ldbl=2:6.2.1+dfsg-1 libgnutls30=3.7.1-1 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-4 libharfbuzz0b=2.7.4-1 libhogweed6=3.7-2.1 libhts-dev=1.11-4 libhts3=1.11-4 libice-dev=2:1.0.10-1 libice6=2:1.0.10-1 libicu-dev=67.1-6 libicu67=67.1-6 libidn2-0=2.3.0-5 libisl23=0.23-1 libitm1=10.2.1-6 libjansson-dev=2.13.1-1.1 libjansson4=2.13.1-1.1 libjbig0=2.1-3.1+b2 libjemalloc-dev=5.2.1-2 libjemalloc2=5.2.1-2 libjpeg62-turbo=1:2.0.6-2 libjq1=1.6-2.1 libjsoncpp24=1.9.4-4 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblapack3=3.9.0-3 libldap-2.4-2=2.4.57+dfsg-2 liblocale-gettext-perl=1.07-4+b1 liblsan0=10.2.1-6 libltdl7=2.4.6-15 liblz4-1=1.9.3-1 liblz4-dev=1.9.3-1 liblzma-dev=5.2.5-2 liblzma5=5.2.5-2 liblzo2-2=2.10-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmd0=1.0.3-3 libmhash2=0.9.9.9-9 libmount-dev=2.36.1-7 libmount1=2.36.1-7 libmpc3=1.2.0-1 libmpdec3=2.5.1-1 libmpfr6=4.1.0-3 libncurses-dev=6.2+20201114-2 libncurses5-dev=6.2+20201114-2 libncurses6=6.2+20201114-2 libncursesw6=6.2+20201114-2 libnettle8=3.7-2.1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libonig5=6.9.6-1.1 libosp5=1.5.2-13+b2 libp11-kit0=0.23.22-1 libpam-modules=1.4.0-6 libpam-modules-bin=1.4.0-6 libpam-runtime=1.4.0-6 libpam0g=1.4.0-6 libpango-1.0-0=1.46.2-3 libpangocairo-1.0-0=1.46.2-3 libpangoft2-1.0-0=1.46.2-3 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpcre16-3=2:8.39-13 libpcre2-16-0=10.36-2 libpcre2-32-0=10.36-2 libpcre2-8-0=10.36-2 libpcre2-dev=10.36-2 libpcre2-posix2=10.36-2 libpcre3=2:8.39-13 libpcre3-dev=2:8.39-13 libpcre32-3=2:8.39-13 libpcrecpp0v5=2:8.39-13 libperl5.32=5.32.1-3 libpipeline1=1.5.3-1 libpixman-1-0=0.40.0-1 libpixman-1-dev=0.40.0-1 libpng-dev=1.6.37-3 libpng16-16=1.6.37-3 libprocps8=2:3.3.17-4 libprotobuf-dev=3.12.4-1 libprotobuf-lite23=3.12.4-1 libprotobuf23=3.12.4-1 libprotoc-dev=3.12.4-1 libprotoc23=3.12.4-1 libpsl5=0.21.0-1.2 libpthread-stubs0-dev=0.4-1 libpython3-stdlib=3.9.2-2 libpython3.9-minimal=3.9.2-1 libpython3.9-stdlib=3.9.2-1 libquadmath0=10.2.1-6 libraptor2-0=2.0.14-1.2 libraptor2-dev=2.0.14-1.2 librasqal3=0.9.33-0.1 librasqal3-dev=0.9.33-0.1 librdf0=1.0.17-1.1+b1 librdf0-dev=1.0.17-1.1+b1 libreadline8=8.1-1 librhash0=1.4.1-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2.1 libsasl2-modules-db=2.1.27+dfsg-2.1 libseccomp2=2.5.1-1 libselinux1=3.1-3 libselinux1-dev=3.1-3 libsepol1=3.1-1 libsepol1-dev=3.1-1 libsigsegv2=2.13-1 libsimde-dev=0.7.2-4 libsm-dev=2:1.2.3-1 libsm6=2:1.2.3-1 libsmartcols1=2.36.1-7 libsmithwaterman-dev=0.0+git20160702.2610e25-11 libsmithwaterman0=0.0+git20160702.2610e25-11 libsparsehash-dev=2.0.3-2 libsqlite3-0=3.34.1-3 libssh2-1=1.9.0-2 libssl1.1=1.1.1j-1 libssw-dev=1.1-13 libssw0=1.1-13 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.3-2 libtabixpp-dev=1.1.0-4 libtabixpp0=1.1.0-4 libtasn1-6=4.16.0-2 libtcl8.6=8.6.11+dfsg-1 libthai-data=0.1.28-4 libthai0=0.1.28-4 libtiff5=4.2.0-1 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtk8.6=8.6.11-2 libtool=2.4.6-15 libtsan0=10.2.1-6 libtsl-hopscotch-map-dev=2.3.0-1 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.3-2 libunistring2=0.9.10-4 libuuid1=2.36.1-7 libuv1=1.40.0-1 libvcflib-dev=1.0.2+dfsg-2 libvcflib-tools=1.0.2+dfsg-2 libvcflib1=1.0.2+dfsg-2 libwebp6=0.6.1-2+b1 libx11-6=2:1.7.0-2 libx11-data=2:1.7.0-2 libx11-dev=2:1.7.0-2 libxau-dev=1:1.0.9-1 libxau6=1:1.0.9-1 libxcb-render0=1.14-3 libxcb-render0-dev=1.14-3 libxcb-shm0=1.14-3 libxcb-shm0-dev=1.14-3 libxcb1=1.14-3 libxcb1-dev=1.14-3 libxdmcp-dev=1:1.1.2-3 libxdmcp6=1:1.1.2-3 libxext-dev=2:1.3.3-1.1 libxext6=2:1.3.3-1.1 libxft2=2.3.2-2 libxml2=2.9.10+dfsg-6.3+b1 libxml2-dev=2.9.10+dfsg-6.3+b1 libxrender-dev=1:0.9.10-1 libxrender1=1:0.9.10-1 libxslt1-dev=1.1.34-4 libxslt1.1=1.1.34-4 libxss1=1:1.2.3-1 libxt6=1:1.2.0-1 libyajl-dev=2.1.0-3 libyajl2=2.1.0-3 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.10.19-1 littler=0.3.12-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 ncal=12.1.7+nmu2 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 opensp=1.5.2-13+b2 openssl=1.1.1j-1 patch=2.7.6-7 perl=5.32.1-3 perl-base=5.32.1-3 perl-modules-5.32=5.32.1-3 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 procps=2:3.3.17-4 protobuf-compiler=3.12.4-1 pv=1.6.6-1+b1 python3=3.9.2-2 python3-distutils=3.9.2-1 python3-lib2to3=3.9.2-1 python3-lxml=4.6.2-1 python3-minimal=3.9.2-2 python3-pkg-resources=52.0.0-3 python3-pygments=2.7.1+dfsg-1 python3.9=3.9.2-1 python3.9-minimal=3.9.2-1 r-base-core=4.0.4-1 r-cran-assertthat=0.2.1-2 r-cran-brio=1.1.1-1 r-cran-callr=3.5.1-1 r-cran-cli=2.3.0-1 r-cran-colorspace=2.0-0+dfsg-1 r-cran-crayon=1.4.0-1 r-cran-desc=1.2.0-3 r-cran-diffobj=0.3.2-1 r-cran-digest=0.6.27-1 r-cran-ellipsis=0.3.1-1 r-cran-evaluate=0.14-2 r-cran-fansi=0.4.2-1 r-cran-farver=2.0.3-1+b1 r-cran-ggplot2=3.3.3+dfsg-1 r-cran-glue=1.4.2-1 r-cran-gridbase=0.4-7-5 r-cran-gtable=0.3.0+dfsg-2 r-cran-isoband=0.2.3-2 r-cran-jsonlite=1.7.2+dfsg-1 r-cran-labeling=0.4.2-1 r-cran-lattice=0.20-41-1+b1 r-cran-lifecycle=0.2.0-2 r-cran-littler=0.3.12-1 r-cran-magrittr=2.0.1-1 r-cran-mass=7.3-53.1-1 r-cran-matrix=1.3-2-1 r-cran-mgcv=1.8-34-1 r-cran-munsell=0.5.0-2 r-cran-nlme=3.1.152-1 r-cran-pillar=1.4.7-1 r-cran-pkgbuild=1.2.0-1 r-cran-pkgconfig=2.0.3-2 r-cran-pkgkitten=0.2.1-1 r-cran-pkgload=1.1.0-1 r-cran-plyr=1.8.6-2 r-cran-praise=1.0.0-4 r-cran-prettyunits=1.1.1-2 r-cran-processx=3.4.5-1 r-cran-ps=1.5.0-1 r-cran-r6=2.5.0-1 r-cran-rcolorbrewer=1.1-2-3 r-cran-rcpp=1.0.6-1 r-cran-rematch2=2.1.2-2 r-cran-rlang=0.4.10-1 r-cran-rprojroot=2.0.2-1 r-cran-rstudioapi=0.13-1 r-cran-scales=1.1.1-1 r-cran-testthat=3.0.1-1 r-cran-tibble=3.0.6+dfsg-1 r-cran-utf8=1.1.4-2 r-cran-vctrs=0.3.6-1 r-cran-viridislite=0.3.0-4 r-cran-waldo=0.2.3-2 r-cran-withr=2.4.1-1 rapidjson-dev=1.1.0+dfsg2-7 raptor2-utils=2.0.14-1.2 rasqal-utils=0.9.33-0.1 readline-common=8.1-1 rs=20200313-1 samtools=1.11-1 sed=4.7-1 sensible-utils=0.0.14 sgml-base=1.30 sgml-data=2.0.11+nmu1 sysvinit-utils=2.96-6 tabix=1.11-4 tar=1.34+dfsg-1 tzdata=2021a-1 ucf=3.0043 unzip=6.0-26 util-linux=2.36.1-7 uuid-dev=2.36.1-7 x11-common=1:7.7+22 x11proto-dev=2020.1-1 x11proto-xext-dev=2020.1-1 xdg-utils=1.1.3-4 xml-core=0.18+nmu1 xorg-sgml-doctools=1:1.11-1.1 xsltproc=1.1.34-4 xtrans-dev=1.4.0-1 xxd=2:8.2.2434-3 xz-utils=5.2.5-2 zip=3.0-12 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210311T143034Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d vg=1.30.0+ds-1 && mkdir -p /build/vg-OlWF3C && dpkg-source --no-check -x /*.dsc /build/vg-OlWF3C/vg-1.30.0+ds && cd /build/vg-OlWF3C/vg-1.30.0+ds && { printf '%s' 'vg (1.30.0+ds-1+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * rebuild for outdated built-using -- amd64 / i386 Build Daemon (x86-ubc-01) Thu, 11 Mar 2021 23:18:13 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/vg-OlWF3C" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/vg-OlWF3C/vg-1.30.0+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1615504693" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/vg-OlWF3C /tmp/vg-1.30.0+ds-1+b164z05hpn bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210311T143034Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.DCQDJyPcwS as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.DCQDJyPcwS Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-7). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210311T143034Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210311T143034Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (715 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4663 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-9) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210311T143034Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.DCQDJyPcwS Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210311T143034Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 20s (1152 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.DCQDJyPcwS I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d vg=1.30.0+ds-1 && mkdir -p /build/vg-OlWF3C && dpkg-source --no-check -x /*.dsc /build/vg-OlWF3C/vg-1.30.0+ds && cd /build/vg-OlWF3C/vg-1.30.0+ds && { printf '%s' 'vg (1.30.0+ds-1+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * rebuild for outdated built-using -- amd64 / i386 Build Daemon (x86-ubc-01) Thu, 11 Mar 2021 23:18:13 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/vg-OlWF3C"' exec /tmp/mmdebstrap.DCQDJyPcwS Reading package lists... NOTICE: 'vg' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/vg.git Please use: git clone https://salsa.debian.org/med-team/vg.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 95.1 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main vg 1.30.0+ds-1 (dsc) [2979 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main vg 1.30.0+ds-1 (tar) [95.0 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main vg 1.30.0+ds-1 (diff) [114 kB] Fetched 95.1 MB in 1min 14s (1281 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'vg_1.30.0+ds-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting vg in /build/vg-OlWF3C/vg-1.30.0+ds dpkg-source: info: unpacking vg_1.30.0+ds.orig.tar.xz dpkg-source: info: unpacking vg_1.30.0+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc-10 dpkg-source: info: applying use_packaged_libdeflate dpkg-source: info: applying use_packaged_jemalloc dpkg-source: info: applying use_packaged_libbackward-cpp dpkg-source: info: applying use_packaged_elfutils dpkg-source: info: applying use_packaged_raptor2 dpkg-source: info: applying no_need_for_snappy dpkg-source: info: applying use_packaged_sparsehash dpkg-source: info: applying use_packaged_ssw dpkg-source: info: applying use_packaged_rapidjson dpkg-source: info: applying use_packaged_fermi-lite dpkg-source: info: applying spelling dpkg-source: info: applying no_rpath dpkg-source: info: applying no_pg dpkg-source: info: applying use_packaged_fastahack dpkg-source: info: applying hardening_flags dpkg-source: info: applying use_packaged_smithwaterman dpkg-source: info: applying static dpkg-source: info: applying use_packaged_lz4 dpkg-source: info: applying parallize_better dpkg-source: info: applying use_packaged_libtsl-hopscotch-map-dev dpkg-source: info: applying libVCFH_unneeded dpkg-source: info: applying better_clean dpkg-source: info: applying use_packaged_vcflib dpkg-source: info: applying use_packaged_htslib dpkg-source: info: applying simde dpkg-source: info: applying crossbuild dpkg-source: info: applying python3 dpkg-source: info: applying fix-handlegraph I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/vg-OlWF3C/vg-1.30.0+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1615504693" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.DCQDJyPcwS dpkg-buildpackage: info: source package vg dpkg-buildpackage: info: source version 1.30.0+ds-1+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-ubc-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' find /build/vg-OlWF3C/vg-1.30.0+ds/include/ -type f -a '!' -name vg_git_version.hpp -delete dh_auto_clean || true make -j10 clean make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd C && make clean cd externalTools && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' rm -rf ../bin ../lib make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cd cutest && make clean cd quicktree_1.1 && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' Makefile:2: ../sdsl-lite/Make.helper: No such file or directory make[3]: *** No rule to make target '../sdsl-lite/Make.helper'. Stop. make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' make[2]: *** [Makefile:691: clean] Error 2 make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' dh_auto_clean: error: make -j10 clean returned exit code 2 make[1]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' debian/rules override_dh_clean make[1]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' rm -Rf ./deps/DYNAMIC/build/CMakeFiles dh_clean make[1]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' dh_autoreconf --sourcedirectory=/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' libtoolize: copying file 'acinclude.d/ltoptions.m4' libtoolize: copying file 'acinclude.d/ltsugar.m4' libtoolize: copying file 'acinclude.d/ltversion.m4' libtoolize: copying file 'acinclude.d/lt~obsolete.m4' configure.ac:15: installing './compile' configure.ac:13: installing './config.guess' configure.ac:13: installing './config.sub' configure.ac:3: installing './install-sh' configure.ac:3: installing './missing' cluster/Makefile.am: installing './depcomp' make[1]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' dh_auto_configure -a debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/debian/help mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/debian/vg/usr mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/debian/vg/usr/lib/vg for SIMD in avx2 avx sse4.1 ssse3 sse3 ; do \ export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -m${SIMD}" && export CFLAGS="-g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -m${SIMD}" && \ make clean ; \ dh_auto_build -- SFX=-${SIMD} all test/build_graph bin/shuf ; \ done make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' Makefile:2: ../sdsl-lite/Make.helper: No such file or directory make[3]: *** No rule to make target '../sdsl-lite/Make.helper'. Stop. make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' make[2]: *** [Makefile:691: clean] Error 2 make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make -j10 "INSTALL=install --strip-program=true" SFX=-avx2 all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" ./install.sh /build/vg-OlWF3C/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp obj/* /build/vg-OlWF3C/vg-1.30.0+ds/obj && cp src/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/vg-OlWF3C/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/vg-OlWF3C/vg-1.30.0+ds/include/ rm -f lib/libboost_* rm -f lib/cleaned_old_protobuf* make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' cp deps/BBHash/BooPHF.h /build/vg-OlWF3C/vg-1.30.0+ds/include rm -Rf include/boost gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' touch lib/cleaned_old_boost make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* rm -Rf include/google/protobuf deps/protobuf cp -r deps/sparsepp/sparsepp include/ make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all Library will be installed in '/build/vg-OlWF3C/vg-1.30.0+ds' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' touch lib/cleaned_old_protobuf_v003 rm -Rf include/dynamic.hpp include/dynamic if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi . ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include/ make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' if [ ! -d obj ]; then mkdir -p obj; fi # annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC && rm -Rf build && mkdir -p build && cd build && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make if [ ! -d lib ]; then mkdir -p lib; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi . ./source_me.sh && cp -r deps/ips4o/ips4o* /build/vg-OlWF3C/vg-1.30.0+ds/include/ find bin obj lib -type f -delete cp ./deps/gfakluge/src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cp ./deps/gfakluge/src/tinyFA/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include/ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi cd ./deps/lru_cache && cp *.h* /build/vg-OlWF3C/vg-1.30.0+ds/include/ make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o if [ ! -d obj ]; then mkdir -p obj; fi cd quicktree_1.1 && make all CC="gcc -std=c99" cp deps/sha1/*.h* /build/vg-OlWF3C/vg-1.30.0+ds/include/ if [ ! -d lib ]; then mkdir -p lib; fi make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/union_find.cpp -o obj/union_find.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o cp deps/progress_bar/progress_bar.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include cp -r deps/dozeu/simde include g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o -- Setting build type to 'Debug' as none was specified. CMake Warning (dev) at /usr/share/cmake-3.18/Modules/GNUInstallDirs.cmake:225 (message): Unable to determine default CMAKE_INSTALL_LIBDIR directory because no target architecture is known. Please enable at least one language before including GNUInstallDirs. Call Stack (most recent call first): CMakeLists.txt:5 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is GNU 10.2.1 -- The C compiler identification is GNU 10.2.1 gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- The CXX compiler identification is GNU 10.2.1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o -- The CXX compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- The C compiler identification is GNU 10.2.1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info -- Detecting C compiler ABI info g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o -- Detecting CXX compiler ABI info - done -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compiler ABI info - done -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting C compiler ABI info g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o -- Detecting CXX compiler ABI info g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h -- Detecting CXX compiler ABI info - done -- Detecting C compiler ABI info - done cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h -- Detecting CXX compiler ABI info - done cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h -- Check for working CXX compiler: /usr/bin/g++ - skipped cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp -- Detecting CXX compile features -- Detecting CXX compile features - done mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG libhandlegraph is root project or external_project -- Configuring done cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp Building in Debug mode -- Configuring done mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp -- Generating done mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘std::size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h -- Generating done cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build --check-build-system CMakeFiles/Makefile.cmake 0 mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build//CMakeFiles/progress.marks cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h make -f CMakeFiles/Makefile2 all -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/depend cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/cw-bwt.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend cp inc/sonLibString.h ../lib/sonLibString.h.tmp make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_bwt.dir/DependInfo.cmake --color= -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp Scanning dependencies of target cw-bwt mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h Scanning dependencies of target handlegraph_objs Scanning dependencies of target rle_bwt make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/build make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/build make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h [ 7%] Building CXX object CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp /usr/bin/c++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/cw-bwt.cpp [ 14%] Building CXX object CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h /usr/bin/c++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/rle_bwt.cpp [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o -- Performing Test HAVE_CXA_DEMANGLE [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o In file included from /usr/include/string.h:495, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. diff: include/vg_environment_version.hpp: No such file or directory g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o -- Looking for C++ include cstdio -- Looking for C++ include cstdio - found [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp -- Configuring done [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Generating done [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp ar rc /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ranlib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/vg-OlWF3C/vg-1.30.0+ds/obj make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wl,-z,relro -Wl,-z,now -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/h0_lz77.dir/DependInfo.cmake --color= make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/benchmark.dir/DependInfo.cmake --color= Scanning dependencies of target benchmark make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 21%] Building CXX object CMakeFiles/benchmark.dir/benchmark.cpp.o Scanning dependencies of target h0_lz77 /usr/bin/c++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/benchmark.dir/benchmark.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/benchmark.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 28%] Building CXX object CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o /usr/bin/c++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/h0_lz77.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ln -s `which shuf` bin/shuf [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp [ 35%] Linking CXX executable cw-bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/cw-bwt.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -o cw-bwt make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 35%] Built target cw-bwt make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_lz77_v2.dir/DependInfo.cmake --color= Scanning dependencies of target rle_lz77_v2 make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 42%] Building CXX object CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o /usr/bin/c++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/rle_lz77_v2.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 50%] Linking CXX executable rle_bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_bwt.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -o rle_bwt cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 50%] Built target rle_bwt make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_lz77_v1.dir/DependInfo.cmake --color= Scanning dependencies of target rle_lz77_v1 make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 57%] Building CXX object CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o /usr/bin/c++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/rle_lz77_v1.cpp [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp [ 64%] Linking CXX executable benchmark /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/benchmark.dir/benchmark.cpp.o -o benchmark make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 64%] Built target benchmark make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/debug.dir/DependInfo.cmake --color= Scanning dependencies of target debug make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 71%] Building CXX object CMakeFiles/debug.dir/debug.cpp.o /usr/bin/c++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/debug.dir/debug.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/debug.cpp [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp [ 83%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm [ 78%] Linking CXX executable h0_lz77 /usr/bin/cmake -E cmake_link_script CMakeFiles/h0_lz77.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -o h0_lz77 make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 85%] Linking CXX executable debug /usr/bin/cmake -E cmake_link_script CMakeFiles/debug.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/debug.dir/debug.cpp.o -o debug [ 85%] Built target h0_lz77 gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm [ 85%] Built target debug [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvw.* /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./autogen.sh || true ./autogen.sh: 22: [[: not found libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest rm -f /build/vg-OlWF3C/vg-1.30.0+ds/include/vg.pb.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' libtoolize: copying file 'acinclude.d/ltoptions.m4' make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' -- The CXX compiler identification is GNU 10.2.1 [ 93%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend libtoolize: copying file 'acinclude.d/ltsugar.m4' make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= Scanning dependencies of target handlegraph_static -- Detecting CXX compiler ABI info make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 libtoolize: copying file 'acinclude.d/ltversion.m4' /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o libtoolize: copying file 'acinclude.d/lt~obsolete.m4' /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= Scanning dependencies of target handlegraph_shared make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -- Detecting CXX compiler ABI info - done [ 92%] Linking CXX executable rle_lz77_v2 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v2.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -o rle_lz77_v2 -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/dozeu && cp deps/dozeu/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/dozeu/ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:321 ] Protobuf_USE_STATIC_LIBS = OFF [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 92%] Built target rle_lz77_v2 [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:455 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:463 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:481 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.4 -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:495 ] /usr/bin/protoc reveals version 3.12.4 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.12.4") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.11-4 -- Checking for module 'jansson' -- Found jansson, version 2.13.1 -- Configuring done -- Generating done [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Scanning dependencies of target link_target make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". Scanning dependencies of target handlegraph make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir [ 4%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download [ 7%] No update step for 'handlegraph' mv ../bin/sonLibTests.tmp ../bin/sonLibTests /usr/bin/cmake -E echo_append make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update [ 9%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 11%] Performing configure step for 'handlegraph' [100%] Linking CXX executable rle_lz77_v1 cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v1.dir/link.txt --verbose=1 . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/vg-OlWF3C/vg-1.30.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -o rle_lz77_v1 Re-run cmake no build system arguments CMake Warning (dev) at /usr/share/cmake-3.18/Modules/GNUInstallDirs.cmake:225 (message): Unable to determine default CMAKE_INSTALL_LIBDIR directory because no target architecture is known. Please enable at least one language before including GNUInstallDirs. Call Stack (most recent call first): CMakeLists.txt:5 (include) This warning is for project developers. Use -Wno-dev to suppress it. make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp -- Detecting C compiler ABI info make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done [100%] Built target rle_lz77_v1 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' # Do the copy of the main file last so we can tell if this recipe failed and redo it. # Otherwise we get dynamic.hpp without its deps mkdir -p include/dynamic && cp -r /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/* include/dynamic -- Detecting CXX compiler ABI info configure.ac:15: installing './compile' make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I .//../sonLib/lib/ -c impl/*.c gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a configure.ac:3: installing './missing' cluster/Makefile.am: installing './depcomp' -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure [ 14%] Performing build step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/depend.internal". Scanning dependencies of target handlegraph_objs make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/handle.cpp checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a checking whether make supports nested variables... rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ yes cp inc/*.h .//../sonLib/lib/ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/depend.internal". Scanning dependencies of target handlegraph_static make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/depend.internal". yes Scanning dependencies of target handlegraph_shared make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake checking whether g++ accepts -g... /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o yes checking whether make supports the include directive... /usr/bin/ranlib libhandlegraph.a make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' yes (GNU style) checking dependency style of g++... make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' gcc3 checking how to run the C++ preprocessor... [100%] Built target handlegraph_shared [100%] Built target handlegraph_static make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 g++ -E make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build [100%] Linking CXX static library libsdsl.a cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 [ 16%] Performing install step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 checking build system type... /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static /usr/bin/ranlib libsdsl.a make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 printf checking for gcc... gcc make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph ranlib -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp checking command to parse /usr/bin/nm -B output from gcc object... -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install [ 19%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done [100%] Built target sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a ok checking for sysroot... no checking for a working dd... make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 21%] Running cpp protocol buffer compiler on deps/vg.proto checking for ANSI C header files... /usr/bin/protoc --cpp_out /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/vg.proto [ 23%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/vg.proto yes checking for sys/types.h... cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Scanning dependencies of target vgio_static make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' yes [ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp [ 28%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc checking for sys/stat.h... [ 30%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o [ 33%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp [ 35%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 38%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp yes checking for stdlib.h... yes checking for string.h... cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". yes Scanning dependencies of target vgio make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 40%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... [ 42%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp yes checking if gcc static flag -static works... [ 45%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... [ 47%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o yes /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... [ 50%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o yes /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... [ 52%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o yes checking for ANSI C header files... (cached) yes checking for boostlib >= 1.0 (100000)... /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp yes checking whether the Boost::Program_Options library is available... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/include'. The library files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! [ 54%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp yes checking for exit in -lboost_program_options... [ 57%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status [ 59%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp [ 61%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 64%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp [ 66%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp [ 69%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp [ 71%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 73%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-OlWF3C/vg-1.30.0+ds/lib config.status: creating vowpalwabbit/config.h [ 76%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp config.status: executing depfiles commands [ 78%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c bwtmerge.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ config.status: executing libtool commands [ 80%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp [ 83%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... [ 85%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp yes checking whether make supports the include directive... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwt.cpp g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... [ 88%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... . ./source_me.sh && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/include:/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" make && cp lib/libbdsg.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-OlWF3C/vg-1.30.0+ds/include gcc -E make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' rm -r bdsg/obj rm -r lib rm -r bin make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' checking for ANSI C header files... g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... [ 90%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E [ 92%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 95%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dynamic_gbwt.cpp yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking whether the Boost::Program_Options library is available... yes checking for main in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c fast_locate.cpp yes checking for joinable pthread attribute... [ 97%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o yes /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' checking that generated files are newer than configure... done configure: creating ./config.status [ 97%] Built target vgio_static rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dbg.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp [100%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib -Wl,-rpath,/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson -lhandlegraph -ldl config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gcsa.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' config.status: creating vowpalwabbit/config.h Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc -- Set runtime path of "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so" to "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/json2pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/registry.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/edit.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/loader.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwt.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ mv -f .deps/vw-main.Tpo .deps/vw-main.Po depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c test.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:57: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:56: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c variants.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_gbwt.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c lcp.cpp In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_ri.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_graph.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c merge_gbwt.cpp In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:41: required from here /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:28, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c benchmark.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata_tool.cpp rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c remove_seq.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwtgraph.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c minimizer.cpp In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:13: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:56: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_cover.cpp In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:75: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:20: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:17: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa2gbwt.cpp In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:29: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = Search::action_repr; size_t = long unsigned int]’: search.cc:1537:22: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:64: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:94: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:36: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:47: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:65: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:65: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:28: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:30: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:32: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:24: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:50: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:17: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:31: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:39: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:151: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o active_interactor active_interactor.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -pthread In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mavx2 -pthread -pthread -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 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csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/vw vw-main.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -pthread make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/vw_exception.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/vw_exception.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ cp: error writing '/build/vg-OlWF3C/vg-1.30.0+ds/lib/libvw.a': No space left on device make[2]: *** [Makefile:503: lib/libvw.a] Error 1 make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' dh_auto_build: error: make -j10 "INSTALL=install --strip-program=true" SFX=-avx2 all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' /tmp/tmp.FiBQVPg4KN/empty.pb.cc: No space left on devicecat: /tmp/tmp.FiBQVPg4KN/empty.pb.h: No such file or directory rm: cannot remove '/tmp/tmp.FiBQVPg4KN/empty.pb.h': No such file or directory rm: cannot remove '/tmp/tmp.FiBQVPg4KN/empty.pb.cc': No such file or directory rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend algorithms.o build_gcsa.o convert_graph.o dbg.o files.o gcsa.o gcsa_format.o internal.o lcp.o path_graph.o support.o try_extend.o utils.o libgcsa2.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/lib' and '/nonexistent/include' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target uninstall-sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" -- Uninstalling 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"/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make -j10 "INSTALL=install --strip-program=true" SFX=-avx all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" ./install.sh /build/vg-OlWF3C/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp obj/* /build/vg-OlWF3C/vg-1.30.0+ds/obj && cp src/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include Library will be installed in '/build/vg-OlWF3C/vg-1.30.0+ds' . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g -c -o obj/gssw.o src/gssw.c . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/vg-OlWF3C/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/vg-OlWF3C/vg-1.30.0+ds/include/ WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all cd quicktree_1.1 && make all CC="gcc -std=c99" if [ ! -d obj ]; then mkdir -p obj; fi rm -f lib/libboost_* rm -f lib/cleaned_old_protobuf* if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' CMake Warning (dev) at /usr/share/cmake-3.18/Modules/GNUInstallDirs.cmake:225 (message): Unable to determine default CMAKE_INSTALL_LIBDIR directory because no target architecture is known. Please enable at least one language before including GNUInstallDirs. Call Stack (most recent call first): CMakeLists.txt:5 (include) This warning is for project developers. Use -Wno-dev to suppress it. rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' if [ ! -d obj ]; then mkdir -p obj; fi make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c if [ ! -d lib ]; then mkdir -p lib; fi make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/union_find.cpp -o obj/union_find.o if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o rm -Rf include/boost rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc libhandlegraph is root project or external_project rm -Rf include/google/protobuf deps/protobuf -- Configuring done touch lib/cleaned_old_boost touch lib/cleaned_old_protobuf_v003 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/stable_double.cpp -o obj/stable_double.o -- The CXX compiler identification is GNU 10.2.1 gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o -- The C compiler identification is GNU 10.2.1 gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c -- Detecting CXX compiler ABI info ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c -- Detecting CXX compiler ABI info - done g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build mv ../lib/avl.h.tmp ../lib/avl.h make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h -- Performing Test HAVE_CXA_DEMANGLE cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o -- Performing Test HAVE_CXA_DEMANGLE - Success [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘std::size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o In file included from /usr/include/string.h:495, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp -- Looking for C++ include cstdio mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp -- Looking for C++ include cstdio - found mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Configuring done [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o ar rc /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp ranlib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/vg-OlWF3C/vg-1.30.0+ds/obj make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp make[2]: 'bin/shuf' is up to date. g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvw.* /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am g++ -Wl,-z,relro -Wl,-z,now -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' rm -f /build/vg-OlWF3C/vg-1.30.0+ds/include/vg.pb.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/ . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./autogen.sh || true [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ./autogen.sh: 22: [[: not found [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp [ 83%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- The CXX compiler identification is GNU 10.2.1 make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Detecting CXX compiler ABI info Scanning dependencies of target sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp -- Detecting CXX compiler ABI info - done cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:321 ] Protobuf_USE_STATIC_LIBS = OFF libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtoolize: copying file 'acinclude.d/ltoptions.m4' -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:455 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:463 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:481 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.4 -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:495 ] /usr/bin/protoc reveals version 3.12.4 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.12.4") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' libtoolize: copying file 'acinclude.d/ltsugar.m4' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C libtoolize: copying file 'acinclude.d/ltversion.m4' [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp libtoolize: copying file 'acinclude.d/lt~obsolete.m4' [ 93%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= -- Found htslib, version 1.11-4 [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ -- Checking for module 'jansson' make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= [ 96%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake -- Found jansson, version 2.13.1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [100%] Built target handlegraph_static [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Configuring done cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Linking CXX static library libsdsl.a cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Generating done make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl*' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: 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/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P 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-S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Scanning dependencies of target link_target Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' Scanning dependencies of target handlegraph make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph [ 2%] Built target link_target make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp [ 4%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/vg.proto /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir [ 7%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download [ 9%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update [ 11%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch [ 14%] Performing configure step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph Re-run cmake no build system arguments -- Configuring done cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C configure.ac:15: installing './compile' configure.ac:3: installing './missing' -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 16%] Performing build step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= Scanning dependencies of target vgio_static make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 19%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o [ 21%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o [ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc [ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp [ 28%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_shared [100%] Built target handlegraph_static make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build [ 30%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 33%] Performing install step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install cluster/Makefile.am: installing './depcomp' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 35%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 38%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp [ 40%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp [ 42%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 42%] Built target handlegraph [ 45%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/include'. The library files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for a thread-safe mkdir -p... [ 47%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... [ 50%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... [ 52%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... [ 54%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp gcc3 checking how to run the C++ preprocessor... . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-OlWF3C/vg-1.30.0+ds/lib [ 57%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp g++ -E /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ checking build system type... . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-OlWF3C/vg-1.30.0+ds/lib x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dbg.cpp /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c bwtmerge.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gcsa.cpp g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ok ranlib sonLib.a checking for sysroot... no checking for a working dd... rm *.o /bin/dd checking how to truncate binary pipes... mv sonLib.a ../lib/ /bin/dd bs=4096 count=1 gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for sys/types.h... yes checking for sys/stat.h... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwt.cpp yes checking for stdlib.h... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for stdint.h... gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dynamic_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c fast_locate.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata.cpp [ 59%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 59%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Scanning dependencies of target vgio make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 61%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c test.cpp GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 64%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking for boostlib >= 1.0 (100000)... yes checking whether the Boost::Program_Options library is available... yes checking for exit in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c variants.cpp yes checking that generated files are newer than configure... done configure: creating ./config.status In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp mv ../bin/sonLibTests.tmp ../bin/sonLibTests gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 66%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands [ 69%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp config.status: executing libtool commands [ 71%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c lcp.cpp checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_graph.cpp yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for gcc option to accept ISO C89... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ none needed checking whether gcc understands -c and -o together... /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking dependency style of gcc... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ gcc3 checking for a sed that does not truncate output... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp yes checking for unistd.h... yes checking for dlfcn.h... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:41: required from here /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:28, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... [ 73%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp yes checking for ANSI C header files... (cached) yes checking whether the Boost::Program_Options library is available... yes checking for main in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_gbwt.cpp PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_ri.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c merge_gbwt.cpp yes checking that generated files are newer than configure... done configure: creating ./config.status In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c benchmark.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 76%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp [ 78%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile [ 80%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata_tool.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c remove_seq.cpp . ./source_me.sh && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/include:/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" make && cp lib/libbdsg.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-OlWF3C/vg-1.30.0+ds/include [ 83%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o [ 85%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp [ 88%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ rm -f lib/libxg.a make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' cp -r deps/xg/src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include rm -r bdsg/obj . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp [ 90%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp [ 92%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 95%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 [ 97%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -Wl,-rpath,/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson handlegraph-prefix/lib/libhandlegraph.so -ldl config.status: creating libvw.pc rm -r lib rm -r bin config.status: creating vowpalwabbit/config.h make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o config.status: executing depfiles commands /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o config.status: executing libtool commands make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/vg-OlWF3C/vg-1.30.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o [100%] Built target vgio make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg rm -f ../vowpalwabbit/*.o rm -f *.lo ar rc 3EdgeConnected.a *.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build rm -f *.lo make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs [100%] Built target vgio rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' Install the project... /usr/bin/cmake -P cmake_install.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I .//../sonLib/lib/ -c impl/*.c -- Install configuration: "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am -- Set runtime path of "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so" to "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/json2pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/registry.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/edit.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/loader.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwtgraph.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa.cpp depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:57: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:56: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c minimizer.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_cover.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa2gbwt.cpp depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:13: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:56: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:29: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = Search::action_repr; size_t = long unsigned int]’: search.cc:1537:22: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:64: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:94: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:36: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:47: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:65: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:65: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:75: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:20: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:17: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:28: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:30: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:32: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:24: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:50: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:17: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:31: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:39: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:151: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o active_interactor active_interactor.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -pthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mavx -pthread -pthread -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ mv -f .deps/vw-main.Tpo .deps/vw-main.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mavx -pthread -pthread -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/vw vw-main.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -pthread make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit/ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:53: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -o bin/vg-avx obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend algorithms.o build_gcsa.o convert_graph.o dbg.o files.o gcsa.o gcsa_format.o internal.o lcp.o path_graph.o support.o try_extend.o utils.o libgcsa2.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/lib' and '/nonexistent/include' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target uninstall-sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make -j10 "INSTALL=install --strip-program=true" SFX=-sse4.1 all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" ./install.sh /build/vg-OlWF3C/vg-1.30.0+ds Library will be installed in '/build/vg-OlWF3C/vg-1.30.0+ds' WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp obj/* /build/vg-OlWF3C/vg-1.30.0+ds/obj && cp src/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/vg-OlWF3C/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/vg-OlWF3C/vg-1.30.0+ds/include/ make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all if [ ! -d lib ]; then mkdir -p lib; fi cd quicktree_1.1 && make all CC="gcc -std=c99" find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' if [ ! -d obj ]; then mkdir -p obj; fi make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' if [ ! -d lib ]; then mkdir -p lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/union_find.cpp -o obj/union_find.o if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi libhandlegraph is root project or external_project g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o -- Configuring done ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o -- Generating done -- The CXX compiler identification is GNU 10.2.1 -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp rm -f lib/libboost_* rm -Rf include/boost gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c touch lib/cleaned_old_boost rm -f lib/cleaned_old_protobuf* gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c ar rc cuTest.a *.o -- The C compiler identification is GNU 10.2.1 ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ -- Detecting CXX compiler ABI info make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc rm -Rf include/google/protobuf deps/protobuf touch lib/cleaned_old_protobuf_v003 [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c -- Detecting CXX compile features -- Detecting CXX compile features - done ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- Detecting C compiler ABI info [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h -- Performing Test HAVE_CXA_DEMANGLE cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp In file included from /usr/include/string.h:495, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/vg-OlWF3C/vg-1.30.0+ds/obj make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp -- Performing Test HAVE_CXA_DEMANGLE - Success mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp cp inc/sonLibList.h ../lib/sonLibList.h.tmp g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h make[2]: 'bin/shuf' is up to date. [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp -- Looking for C++ include cstdio - found mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp g++ -Wl,-z,relro -Wl,-z,now -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvw.* /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h rm -f /build/vg-OlWF3C/vg-1.30.0+ds/include/vg.pb.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h cp inc/stGraph.h ../lib/stGraph.h.tmp -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) mv ../lib/stGraph.h.tmp ../lib/stGraph.h . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/ cp inc/stJson.h ../lib/stJson.h.tmp cp inc/stMatrix.h ../lib/stMatrix.h.tmp [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h mv ../lib/stJson.h.tmp ../lib/stJson.h . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./autogen.sh || true g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h ./autogen.sh: 22: [[: not found gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- The CXX compiler identification is GNU 10.2.1 -- Detecting CXX compiler ABI info # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz -- Configuring done -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz -- Generating done impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz Scanning dependencies of target sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:321 ] Protobuf_USE_STATIC_LIBS = OFF [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp libtoolize: copying file 'acinclude.d/ltoptions.m4' libtoolize: copying file 'acinclude.d/ltsugar.m4' libtoolize: copying file 'acinclude.d/ltversion.m4' [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o libtoolize: copying file 'acinclude.d/lt~obsolete.m4' [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:455 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:463 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:481 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.4 -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:495 ] /usr/bin/protoc reveals version 3.12.4 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.12.4") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ -- Found htslib, version 1.11-4 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ -- Checking for module 'jansson' In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ -- Found jansson, version 2.13.1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp -- Configuring done cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o -- Generating done g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Scanning dependencies of target link_target make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". Scanning dependencies of target handlegraph make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘std::size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o [ 4%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download [ 7%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update [ 9%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch [ 11%] Performing configure step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph Re-run cmake no build system arguments -- Configuring done -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o [ 14%] Performing build step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= [ 83%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build [ 16%] Performing install step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 19%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 21%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/vg.proto [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C Scanning dependencies of target vgio_static Scanning dependencies of target vgio make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build [ 23%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 26%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rc /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ [ 28%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp [ 93%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ configure.ac:15: installing './compile' configure.ac:3: installing './missing' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o cluster/Makefile.am: installing './depcomp' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 30%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp checking whether the C++ compiler works... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for C++ compiler default output file name... a.out checking for suffix of executables... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking whether we are cross compiling... no checking for suffix of object files... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ yes (GNU style) /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ checking dependency style of g++... /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc3 checking how to run the C++ preprocessor... g++ -E cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking build system type... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 33%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp checking for ANSI C header files... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ checking for string.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for memory.h... yes checking for strings.h... [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 35%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp no checking dynamic linker characteristics... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 38%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest [ 40%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest [ 42%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp yes checking if g++ static flag -static works... [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp yes checking if g++ supports -c -o file.o... [ 45%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp [ 47%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking for boostlib >= 1.0 (100000)... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking whether the Boost::Program_Options library is available... [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp yes [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp checking for exit in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... [ 50%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp yes [ 52%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp checking that generated files are newer than configure... done configure: creating ./config.status In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp [ 54%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp [ 57%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp [ 59%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp [ 61%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 64%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' [ 66%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp [ 69%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 71%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 73%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp [ 76%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/vg-OlWF3C/vg-1.30.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c [ 78%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp [ 80%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a config.status: creating Makefile rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I .//../sonLib/lib/ -c impl/*.c config.status: creating vowpalwabbit/config.h [ 83%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -Wl,-rpath,/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson handlegraph-prefix/lib/libhandlegraph.so -ldl config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [100%] Linking CXX static library libsdsl.a cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes [ 85%] Built target vgio checking for a thread-safe mkdir -p... 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[ 92%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... [ 95%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o yes (GNU style) checking dependency style of g++... /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp gcc3 [100%] Built target sdsl checking how to run the C++ preprocessor... make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks g++ -E make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build ar rc stPinchesAndCacti.a *.o make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' ranlib stPinchesAndCacti.a checking build system type... rm *.o [100%] Built target sdsl mv stPinchesAndCacti.a .//../sonLib/lib/ make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 cp inc/*.h .//../sonLib/lib/ gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... 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/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: 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/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... [ 97%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/include'. The library files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-OlWF3C/vg-1.30.0+ds/lib . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-OlWF3C/vg-1.30.0+ds/lib . ./source_me.sh && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/include:/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" make && cp lib/libbdsg.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-OlWF3C/vg-1.30.0+ds/include rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include checking for unistd.h... . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' rm -r bdsg/obj rm -r lib rm -r bin make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dbg.cpp yes make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' checking for dlfcn.h... rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c bwtmerge.cpp yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwt.cpp no checking dynamic linker characteristics... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E [100%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/ranlib libvgio.a checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dynamic_gbwt.cpp make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking whether the Boost::Program_Options library is available... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [100%] Built target vgio_static make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' Install the project... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so -- Set runtime path of "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so" to "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a yes checking for main in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/json2pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/registry.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/edit.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/loader.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o yes g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o checking that generated files are newer than configure... done configure: creating ./config.status /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c fast_locate.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gcsa.cpp config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:57: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:56: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c lcp.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_graph.cpp depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:41: required from here /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:28, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c test.cpp depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c variants.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_ri.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c merge_gbwt.cpp depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:56: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c benchmark.cpp In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:13: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata_tool.cpp In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c remove_seq.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:29: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = Search::action_repr; size_t = long unsigned int]’: search.cc:1537:22: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:64: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:94: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:36: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:47: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:65: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:65: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:75: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:20: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:17: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:28: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs 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-Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:30: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:32: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:24: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwtgraph.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c minimizer.cpp depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_cover.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:50: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa2gbwt.cpp depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:31: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:39: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:17: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:151: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src 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-ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman 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-g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time 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allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o active_interactor active_interactor.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -msse4.1 -pthread -pthread -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ mv -f .deps/vw-main.Tpo .deps/vw-main.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -msse4.1 -pthread -pthread -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/vw vw-main.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -pthread make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit/ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:53: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -o bin/vg-sse4.1 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend algorithms.o build_gcsa.o convert_graph.o dbg.o files.o gcsa.o gcsa_format.o internal.o lcp.o path_graph.o support.o try_extend.o utils.o libgcsa2.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/lib' and '/nonexistent/include' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target uninstall-sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make -j10 "INSTALL=install --strip-program=true" SFX=-ssse3 all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp" ./install.sh /build/vg-OlWF3C/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp obj/* /build/vg-OlWF3C/vg-1.30.0+ds/obj && cp src/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/vg-OlWF3C/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/vg-OlWF3C/vg-1.30.0+ds/include/ Library will be installed in '/build/vg-OlWF3C/vg-1.30.0+ds' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' rm -f lib/libboost_* gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c rm -f lib/cleaned_old_protobuf* make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all cd quicktree_1.1 && make all CC="gcc -std=c99" find bin obj lib -type f -delete make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' rm -Rf include/boost rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' if [ ! -d obj ]; then mkdir -p obj; fi touch lib/cleaned_old_boost if [ ! -d lib ]; then mkdir -p lib; fi make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -Rf include/google/protobuf deps/protobuf gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/union_find.cpp -o obj/union_find.o touch lib/cleaned_old_protobuf_v003 gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o libhandlegraph is root project or external_project -- Configuring done gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/vg-OlWF3C/vg-1.30.0+ds/obj make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp -- The CXX compiler identification is GNU 10.2.1 make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp -- The C compiler identification is GNU 10.2.1 -- Detecting CXX compiler ABI info [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp make[2]: 'bin/shuf' is up to date. g++ -Wl,-z,relro -Wl,-z,now -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp -- Detecting CXX compiler ABI info - done mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp -- Detecting C compiler ABI info mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h In file included from /usr/include/string.h:495, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp -- Detecting C compiler ABI info - done mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h -- Compiler is recent enough to support C++11. mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG cp inc/sonLibString.h ../lib/sonLibString.h.tmp [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvw.* /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac rm -f /build/vg-OlWF3C/vg-1.30.0+ds/include/vg.pb.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/ cp inc/stGraph.h ../lib/stGraph.h.tmp . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am mv ../lib/stGraph.h.tmp ../lib/stGraph.h . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am cp inc/stJson.h ../lib/stJson.h.tmp . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./autogen.sh || true ./autogen.sh: 22: [[: not found mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h -- The CXX compiler identification is GNU 10.2.1 cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ -- Performing Test HAVE_CXA_DEMANGLE g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o -- Detecting CXX compiler ABI info # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘std::size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o ar rvs lib/libgssw.a obj/gssw.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o ar: creating lib/libgssw.a a - obj/gssw.o [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' -- Looking for C++ include cstdio - found -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:321 ] Protobuf_USE_STATIC_LIBS = OFF libtoolize: copying file 'acinclude.d/ltoptions.m4' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C libtoolize: copying file 'acinclude.d/ltsugar.m4' libtoolize: copying file 'acinclude.d/ltversion.m4' -- Configuring done [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp libtoolize: copying file 'acinclude.d/lt~obsolete.m4' -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:455 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:463 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:481 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.4 -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:495 ] /usr/bin/protoc reveals version 3.12.4 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.12.4") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp -- Found htslib, version 1.11-4 -- Checking for module 'jansson' -- Found jansson, version 2.13.1 [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Configuring done -- Generating done cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Scanning dependencies of target link_target make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". Scanning dependencies of target handlegraph make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /usr/bin/cmake -E make_directory 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echo_append [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C Scanning dependencies of target sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory 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-ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp ar rc /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Performing build step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build [ 16%] Performing install step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install [ 19%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 21%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/vg.proto make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 23%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/vg.proto cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [100%] Linking CXX static library libsdsl.a cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Scanning dependencies of target vgio make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 26%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp [ 33%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o [ 33%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o [ 33%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o [ 35%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 38%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 40%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp [ 42%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp [ 45%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp [ 47%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp [ 50%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp [ 52%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 54%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Scanning dependencies of target vgio_static make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [100%] Built target sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl*' [ 57%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc [ 93%] Built target handlegraph_objs -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a [ 96%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= [ 59%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C configure.ac:15: installing './compile' configure.ac:3: installing './missing' make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 61%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp [ 64%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles 0 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cluster/Makefile.am: installing './depcomp' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 66%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp [ 69%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp [ 71%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 73%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 76%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... [ 78%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -Wl,-rpath,/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson handlegraph-prefix/lib/libhandlegraph.so -ldl checking whether we are cross compiling... [ 83%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o [ 83%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... [ 85%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking dependency style of gcc... [ 85%] Built target vgio cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc3 checking for a sed that does not truncate output... [ 88%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... [ 90%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... [ 92%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/include'. The library files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-OlWF3C/vg-1.30.0+ds/lib @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ gcc -E checking for ANSI C header files... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dbg.cpp yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for strings.h... yes checking for inttypes.h... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp yes /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gcsa.cpp checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 95%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... [ 97%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for ANSI C header files... (cached) yes checking for boostlib >= 1.0 (100000)... yes checking whether the Boost::Program_Options library is available... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c lcp.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for exit in -lboost_program_options... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_graph.cpp yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-OlWF3C/vg-1.30.0+ds/lib In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [100%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp /usr/bin/ranlib libvgio.a cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:41: required from here /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:28, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ [100%] Built target vgio_static make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= Scanning dependencies of target vgio make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 61%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c bwtmerge.cpp config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ config.status: creating libvw.pc In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwt.cpp checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc . ./source_me.sh && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/include:/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp" make && cp lib/libbdsg.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-OlWF3C/vg-1.30.0+ds/include make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' rm -r bdsg/obj rm -r lib gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ rm -r bin /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' checking whether we are using the GNU C compiler... make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dynamic_gbwt.cpp [ 64%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking whether the Boost::Program_Options library is available... [ 66%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp yes checking for main in -lboost_program_options... g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c fast_locate.cpp [ 69%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -Wl,-rpath,/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson handlegraph-prefix/lib/libhandlegraph.so -ldl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o [100%] Built target vgio make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) mv ../bin/sonLibTests.tmp ../bin/sonLibTests gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm rm -f stamp-h1 mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest touch config.h.in make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd .. && /bin/bash ./config.status vowpalwabbit/config.h g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o -- Set runtime path of "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so" to "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwt.cpp In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c test.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/json2pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/registry.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/edit.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/loader.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c variants.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_ri.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:57: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:56: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c merge_gbwt.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c benchmark.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata_tool.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c remove_seq.cpp depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\ mv -f $depbase.Tpo $depbase.Plo make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:56: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:13: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:29: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = Search::action_repr; size_t = long unsigned int]’: search.cc:1537:22: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:64: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:94: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:36: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:47: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:65: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:65: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:75: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:20: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:17: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:28: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:30: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:32: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:24: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:50: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/vg-OlWF3C/vg-1.30.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I .//../sonLib/lib/ -c impl/*.c In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:17: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:31: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:39: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:151: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c minimizer.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_cover.cpp depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa2gbwt.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mssse3 -pthread -pthread -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o active_interactor active_interactor.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -pthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' mv -f .deps/vw-main.Tpo .deps/vw-main.Po libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mssse3 -pthread -pthread -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/vw vw-main.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -pthread make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit/ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:53: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -o bin/vg-ssse3 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend algorithms.o build_gcsa.o convert_graph.o dbg.o files.o gcsa.o gcsa_format.o internal.o lcp.o path_graph.o support.o try_extend.o utils.o libgcsa2.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/lib' and '/nonexistent/include' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target uninstall-sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make -j10 "INSTALL=install --strip-program=true" SFX=-sse3 all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" ./install.sh /build/vg-OlWF3C/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp obj/* /build/vg-OlWF3C/vg-1.30.0+ds/obj && cp src/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/vg-OlWF3C/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/vg-OlWF3C/vg-1.30.0+ds/include/ make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' rm -f lib/libboost_* rm -f lib/cleaned_old_protobuf* make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' Library will be installed in '/build/vg-OlWF3C/vg-1.30.0+ds' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c if [ ! -d obj ]; then mkdir -p obj; fi make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all cd quicktree_1.1 && make all CC="gcc -std=c99" if [ ! -d lib ]; then mkdir -p lib; fi make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -Rf include/boost find bin obj lib -type f -delete WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi touch lib/cleaned_old_boost rm -Rf include/google/protobuf deps/protobuf if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi touch lib/cleaned_old_protobuf_v003 gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o if [ ! -d lib ]; then mkdir -p lib; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/union_find.cpp -o obj/union_find.o libhandlegraph is root project or external_project gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c -- Configuring done ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/vg-OlWF3C/vg-1.30.0+ds/obj make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp -- Generating done g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp make[2]: 'bin/shuf' is up to date. -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend -- The CXX compiler identification is GNU 10.2.1 make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o -- The C compiler identification is GNU 10.2.1 ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- Detecting CXX compiler ABI info g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o g++ -Wl,-z,relro -Wl,-z,now -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvw.* /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./autogen.sh || true ./autogen.sh: 22: [[: not found -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h -- Performing Test HAVE_CXA_DEMANGLE libtoolize: copying file 'acinclude.d/ltoptions.m4' cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp libtoolize: copying file 'acinclude.d/ltsugar.m4' mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp libtoolize: copying file 'acinclude.d/ltversion.m4' cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp In file included from /usr/include/string.h:495, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C libtoolize: copying file 'acinclude.d/lt~obsolete.m4' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp -- Looking for C++ include cstdio cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o -- Looking for C++ include cstdio - found rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) rm -f /build/vg-OlWF3C/vg-1.30.0+ds/include/vg.pb.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install -- Configuring done /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp -- Generating done [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp -- The CXX compiler identification is GNU 10.2.1 -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build -- Detecting CXX compiler ABI info make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘std::size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ Scanning dependencies of target sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:321 ] Protobuf_USE_STATIC_LIBS = OFF g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:455 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:463 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:481 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.4 -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:495 ] /usr/bin/protoc reveals version 3.12.4 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.12.4") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp -- Found htslib, version 1.11-4 -- Checking for module 'jansson' -- Found jansson, version 2.13.1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' -- Configuring done configure.ac:15: installing './compile' configure.ac:3: installing './missing' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cluster/Makefile.am: installing './depcomp' [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Generating done /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Scanning dependencies of target link_target make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". Scanning dependencies of target handlegraph make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ [ 4%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download [ 7%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 9%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 11%] Performing configure step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph Re-run cmake no build system arguments -- Configuring done In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... -- Generating done [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure yes (GNU style) checking dependency style of g++... [ 14%] Performing build step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks gcc3 checking how to run the C++ preprocessor... make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend g++ -E make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend checking build system type... make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build printf checking for gcc... gcc [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp [ 16%] Performing install step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks checking whether we are using the GNU C compiler... make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= yes checking whether gcc accepts -g... make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build yes checking for gcc option to accept ISO C89... make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 none needed checking whether gcc understands -c and -o together... make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp yes checking dependency style of gcc... make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install gcc3 checking for a sed that does not truncate output... /bin/sed [ 19%] Completed 'handlegraph' checking for grep that handles long lines and -e... /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 21%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/vg.proto yes checking for memory.h... cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". yes checking for strings.h... Scanning dependencies of target vgio_static make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 23%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc yes checking for inttypes.h... yes cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking if gcc supports -c -o file.o... [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp GNU/Linux ld.so checking how to hardcode library paths into programs... immediate make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend checking whether stripping libraries is possible... make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Scanning dependencies of target vgio make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' checking how to run the C++ preprocessor... g++ -E [ 26%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes [ 28%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking if g++ static flag -static works... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o yes checking if g++ supports -c -o file.o... [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking for boostlib >= 1.0 (100000)... yes checking whether the Boost::Program_Options library is available... ar rc /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' [ 83%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp yes [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp checking for exit in -lboost_program_options... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for joinable pthread attribute... [ 30%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking that generated files are newer than configure... done configure: creating ./config.status [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' config.status: creating Makefile config.status: creating vowpalwabbit/Makefile cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... [ 33%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... [ 93%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' yes checking for sys/types.h... [ 96%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 yes /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o checking for sys/stat.h... /usr/bin/ranlib libhandlegraph.a yes checking for stdlib.h... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' yes checking for string.h... yes make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= checking for memory.h... make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o yes checking for strings.h... yes checking for inttypes.h... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target handlegraph_static [ 35%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp yes make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles 0 [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp yes checking if gcc static flag -static works... make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' yes checking if gcc supports -c -o file.o... cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp [ 38%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes ranlib sonLib.a checking how to run the C++ preprocessor... g++ -E rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 [ 40%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm yes checking if g++ static flag -static works... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking if g++ supports -c -o file.o... [ 42%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking whether the Boost::Program_Options library is available... gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm yes checking for main in -lboost_program_options... [ 45%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp [ 47%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp [ 50%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp [ 52%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest yes checking if zlib is wanted... [ 54%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp [ 57%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes [ 59%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp checking that generated files are newer than configure... done configure: creating ./config.status [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 61%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile [ 64%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp config.status: executing depfiles commands [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 66%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 69%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -Wl,-rpath,/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson handlegraph-prefix/lib/libhandlegraph.so -ldl [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 71%] Built target vgio depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o [ 73%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo [ 76%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:57: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:56: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o [ 78%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o [ 80%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 83%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/vg-OlWF3C/vg-1.30.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp [ 85%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I .//../sonLib/lib/ -c impl/*.c libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp [ 88%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp [ 90%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a [ 92%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp [ 95%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 97%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 [100%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [100%] Linking CXX static library libsdsl.a cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target vgio_static make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [100%] Built target sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: 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/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o -- Set runtime path of "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so" to "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:13: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/include'. The library files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/json2pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/registry.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/edit.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/loader.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-OlWF3C/vg-1.30.0+ds/lib libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dbg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:56: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gcsa.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:29: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = Search::action_repr; size_t = long unsigned int]’: search.cc:1537:22: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:64: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:94: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:36: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:47: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:65: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:65: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:75: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:20: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:17: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c lcp.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_graph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:41: required from here /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:28, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:28: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c bwtmerge.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwt.cpp In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' . ./source_me.sh && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/include:/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" make && cp lib/libbdsg.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-OlWF3C/vg-1.30.0+ds/include libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' rm -r bdsg/obj rm -r lib rm -r bin make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dynamic_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c fast_locate.cpp depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:30: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:32: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:24: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata.cpp depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c test.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c variants.cpp depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_ri.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c merge_gbwt.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c benchmark.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata_tool.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c remove_seq.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:50: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwtgraph.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c minimizer.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_cover.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa2gbwt.cpp depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:17: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:31: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:39: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:151: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o active_interactor active_interactor.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -pthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -msse3 -pthread -pthread -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 mv -f .deps/vw-main.Tpo .deps/vw-main.Po libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -msse3 -pthread -pthread -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/vw vw-main.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -pthread make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit/ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:53: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -o bin/vg-sse3 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' CXXFLAGS="-g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3" CFLAGS="-g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3" dh_auto_build -- SFX=-plain all test/build_graph bin/shuf make -j10 "INSTALL=install --strip-program=true" SFX=-plain all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" ./install.sh /build/vg-OlWF3C/vg-1.30.0+ds Library will be installed in '/build/vg-OlWF3C/vg-1.30.0+ds' WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[2]: 'bin/shuf' is up to date. -- The CXX compiler identification is GNU 10.2.1 -- The C compiler identification is GNU 10.2.1 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success -- Performing Test HAVE_CXA_DEMANGLE -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio -- Looking for C++ include cstdio - found -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [100%] Linking CXX static library libsdsl.a cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/include'. The library files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-OlWF3C/vg-1.30.0+ds/lib . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-OlWF3C/vg-1.30.0+ds/lib . ./source_me.sh && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/include:/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" make && cp lib/libbdsg.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-OlWF3C/vg-1.30.0+ds/include rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata rm -r bdsg/obj rm -r lib rm -r bin make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c bwtmerge.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dynamic_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c fast_locate.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwt.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c test.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c variants.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_ri.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c merge_gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c benchmark.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata_tool.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c remove_seq.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c minimizer.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_cover.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa2gbwt.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:53: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -o bin/vg-plain obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' cp bin/vg-plain debian/help/vg PATH=$PATH:/build/vg-OlWF3C/vg-1.30.0+ds/debian/help \ help2man \ --no-discard-stderr \ --no-info \ --help-option=help \ --version-option=version \ --name='tools for working with genome variation graphs' \ vg > debian/vg.1 make[1]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' dh_install debian/bin/simd-dispatch /usr/lib/vg/ dh_install bin/vg* usr/lib/vg/ mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/debian/vg/usr/bin cd /build/vg-OlWF3C/vg-1.30.0+ds/debian/vg/usr/bin \ && for prog in vg ; do \ ln -s ../lib/vg/simd-dispatch ${prog} ; done make[1]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dwz: Too few files for multifile optimization dh_dwz: warning: No dwz multifile created, but not explicitly requested either so ignoring it. dh_dwz: warning: Common issues include no debug information at all (missing -g) and dh_dwz: warning: compressed debug information (#931891). dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a debian/rules override_dh_gencontrol make[1]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-4), " make[1]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'vg-dbgsym' in '../vg-dbgsym_1.30.0+ds-1+b1_amd64.deb'. dpkg-deb: building package 'vg' in '../vg_1.30.0+ds-1+b1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../vg_1.30.0+ds-1+b1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/vg-OlWF3C /tmp/vg-1.30.0+ds-1+b164z05hpn I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.DCQDJyPcwS... I: success in 8618.6109 seconds md5: Value of 'md5' differs for vg-dbgsym_1.30.0+ds-1+b1_amd64.deb md5: Size differs for vg-dbgsym_1.30.0+ds-1+b1_amd64.deb md5: Value of 'md5' differs for vg_1.30.0+ds-1+b1_amd64.deb md5: Size differs for vg_1.30.0+ds-1+b1_amd64.deb sha1: Value of 'sha1' differs for vg-dbgsym_1.30.0+ds-1+b1_amd64.deb sha1: Size differs for vg-dbgsym_1.30.0+ds-1+b1_amd64.deb sha1: Value of 'sha1' differs for vg_1.30.0+ds-1+b1_amd64.deb sha1: Size differs for vg_1.30.0+ds-1+b1_amd64.deb sha256: Value of 'sha256' differs for vg-dbgsym_1.30.0+ds-1+b1_amd64.deb sha256: Size differs for vg-dbgsym_1.30.0+ds-1+b1_amd64.deb sha256: Value of 'sha256' differs for vg_1.30.0+ds-1+b1_amd64.deb sha256: Size differs for vg_1.30.0+ds-1+b1_amd64.deb Checksums: FAIL Cannot generate diffoscope for vg-dbgsym_1.30.0+ds-1+b1_amd64.deb: Cannot find URL: http://snapshot.notset.fr/mr/file/bf930626712774356032629006f312c29bea1232e229d87f37ce16cc26d209d8/download Cannot generate diffoscope for vg_1.30.0+ds-1+b1_amd64.deb: RetryError[]